METTL18-mediated histidine methylation of RPL3 modulates translation elongation for proteostasis maintenance

Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a methylation substrate. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood to date. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traversal on Tyr codons, allowing the proper folding of synthesized proteins. By performing an in vitro methylation assay with a methyl donor analog and quantitative mass spectrometry, we found that His245 of RPL3 is methylated at the τ-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed stoichiometric modification and suggested a role in translation reactions. Indeed, genome-wide ribosome profiling and an in vitro translation assay revealed that translation elongation at Tyr codons was suppressed by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from the cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of a ribosome modification that ensures proteome integrity in cells.


Introduction
Protein methylation is an integral post-translational modification (PTM) that contributes to the critical role of epigenetics. This modification influences the function of proteins and provides a convertible platform for the modulation of cellular processes, including interactions with other molecules, protein structure, localization, and enzymatic activity (Biggar and Li, 2015;Clarke, 2018;Murn and Shi, 2017;Rodríguez-Paredes and Lyko, 2019). Whereas the majority of protein methylation has been observed on lysine and arginine amino acids (Biggar and Li, 2015;Clarke, 2018;Murn and Shi, 2017;Rodríguez-Paredes and Lyko, 2019), histidine residues also supply alternative target sites for methylation. Although this modification was previously thought to be restricted to limited proteins (Webb et al., 2010), a recent comprehensive survey suggested widespread occurrence in the proteome Ning et al., 2016;Wilkinson et al., 2019).
Recent emerging studies have shown that the ribosome is a hotspot for PTM (Emmott et al., 2019;Simsek and Barna, 2017). This led to the idea of gene regulation through the decorated ribosomes. Indeed, PTMs on ribosomal proteins may regulate protein synthesis in specific contexts, such as a subset of transcripts (Imami et al., 2018;Kapasi et al., 2007;Mazumder et al., 2003), the cell cycle (Imami et al., 2018), stress response (Higgins et al., 2015;Matsuki et al., 2020), and differentiation (Werner et al., 2015).
In this work, we studied the previously uncharacterized methyltransferase METTL18. Through a survey of the substrate, we found that this protein catalyzes τ-N-methylation on His245 of the ribosomal protein large subunit (RPL) 3 (uL3 as universal nomenclature). Cryo-electron microscopy (cryo-EM) suggested that τ-N-methylation interferes with the interaction of His245, which is located close to the peptidyl transferase center (PTC), with G1595 in the loop of helix 35 in 28S rRNA. Genomewide ribosome profiling revealed that the τ-N-methylhistidine on RPL3 retards translation elongation at Tyr codons, a conclusion that was also supported by an in vitro translation assay. Quantitative proteome analysis showed that slower elongation is associated with the proper folding of synthesized proteins and thus ensures healthy proteostasis in cells; otherwise, proteins are aggregated and degraded. Our study provided an example of a modified ribosome as a nexus for the quality control of synthesized protein.

METTL18 is a histidine τ-N-methyltransferase
To overview τ-N-histidine methylation in cells and the corresponding enzymes, we quantified τ-Nmethylhistidine by mass spectrometry (MS). To distinguish the two types of histidine methylations, we performed multiple reaction monitoring (MRM) of digested amino acids to trace specific m/z transitions from the precursor ) (see 'Materials and methods' section for details). Because SETD3 modifies abundant actin proteins Guo et al., 2019;Kwiatkowski et al., 2018;Wilkinson et al., 2019;Zheng et al., 2020), SETD3 knockout (KO) in HEK293T cells (Figure 1-figure supplement 1B-E) greatly reduced τ-N-methylhistidine ( Figure 1A). However, a substantial fraction of τ-N-methylhistidine was left in the SETD3 KO cells ( Figure 1A), suggesting the presence of other mammalian τ-N-methyltransferase(s).

METTL18 catalyzes τ-N-methylation on His245 in RPL3
These observations led us to survey the methylation substrate of METTL18. For this purpose, we harnessed propargylic Se-adenosyll-selenomethionine (ProSeAM), an analog of S-adenosyllmethionine (SAM). This compound acts as a donor in the methylation reaction by the SET domain and 7-β-strand methyltransferase Shimazu et al., 2014;Shimazu et al., 2018). Instead of a methyl moiety, a propargyl unit was added to the substrate residue, allowing biotin tagging with a click reaction Shimazu et al., 2014;Shimazu et al., 2018; Figure 1B). Using ProSeAM, we performed in vitro methylation with recombinant METTL18 (Figure 1-figure supplement 1G) in the lysate of METTL18 KO cells and detected the ProSeAMreacted proteins in a METTL18 protein-dependent manner ( Figure 1C). The high background signals are likely to have originated from methyltransferases other than METTL18 in the lysate. For the quantitative and sensitive proteomic identification of methylated protein(s), we combined this approach with stable isotope labeling using amino acids in cell culture (SILAC) ( Figure 1B). ProSeAM was added to the cell lysates of METTL18 KO cells labeled with either light or heavy isotopic amino acids. Only the extract from heavy-isotope-labeled cells was incubated with recombinant METTL18 ( Figure 1B). After lysate pooling and streptavidin purification ( Figure 1B), isolated proteins were quantitatively assessed by liquid chromatography (LC)-MS/MS. Among the detected proteins, human RPL3 was the only candidate to be reproducibly identified ( Figure 1D).
To ensure cellular histidine methylation on the protein, FLAG-tagged RPL3 was expressed in naïve HEK293T cells, immunopurified, and subjected to LC-MS/MS. This analysis identified the methylhistidine in cellular RPL3 and precisely annotated the residue at His245 ( Figure 1E). In stark contrast, the same experiments with METTL18 KO did not detect methylated His245 ( Figure 1F). The ectopic expression of wild-type (WT) METTL18 in the KO cells rescued the modification, whereas mutations in the potential SAM binding site (Asp193Lys-Gly195Arg-Gly197Arg), which were predicted based on lysine methyltransferase orthologs (Ng et al., 2002), abolished the potential ( Figure 1F). The same METTL18-dependent His245 methylation was also found in endogenous RPL3 (Figure 1 -figure supplement 2C and D), isolated in the 60S subunit ( Figure 1-figure supplement 2A and B).
To distinguish the methylation forms on histidine, we applied MRM to the peptide fragments containing His245 and clearly observed that methylation occurs at the τ-N position but not at the π-N position ( Figure 1G).
Thus, taken together, our data demonstrated that His245 of RPL3 is a METTL18 substrate for the formation of τ-N-methylhistidine in cells.
The online version of this article includes the following source data and figure supplement(s) for figure 1: Source data 1. Full and unedited blots corresponding to Figure 1C.
Source data 2. Primary data for graphs in Figure 1.         METTL18 associates with early pre-60S As RPL3 in crude lysate was methylated in vitro ( Figure 1C and D), we set out to recapitulate this reaction by purified factors using 14 C-labeled SAM as a methyl donor. Irrespective of the human or mouse homolog, the immunopurified FLAG-tagged RPL3 proteins transiently expressed in METTL18 KO cells were efficiently labeled by recombinant METTL18 (Figure 2A). Moreover, changing His245 to Ala completely abolished the reaction, validating His245 as a methylation site. In contrast, recombinant RPL3 expressed in bacteria was a poor substrate ( Figure 2A). A similar deficiency in the in vitro methylation assay by Hpm1 on solo RPL3 protein produced in bacteria was seen in yeast (Al-Hadid et al., 2014). Given that RPL3 expressed in mammalian cells assembled into ribosomes but RPL3 expressed in bacteria did not, we hypothesized that METTL18 recognizes RPL3 within ribosomes or preassembled intermediates. To characterize the molecular complex associated with METTL18, we separated the ribosomal complexes through a sucrose density gradient and found that METTL18 was associated with a complex smaller than mature 60S ( Figure 2B). Given the smaller size, we speculated that the METTL18-associating complex is pre-60S in the middle of biogenesis. Indeed, the METTL18-containing subfractions also possessed PES1 (a yeast Nop7 homolog), a ribosome biogenesis factor at an early step (Kater et al., 2017;Sanghai et al., 2018), and a small portion of RPL3 ( Figure 2B). On the other hand, NMD3, an adaptor protein of the late-stage pre-60S for cytoplasmic export (Ma et al., 2017;Malyutin et al., 2017), was almost exclusive to the METTL18associating pre-60S. These data suggested that RPL3, in an early intermediate complex of 60S biogenesis, is an efficient substrate for METTL18.  , no altered abundance of the 60S subunit (relative to the 40S subunit) was observed in METTL18 KO cells, while the knockdown of RPL17, which is known to hamper 60S biogenesis (Wang et al., 2015), reduced the 60S abundance in a sucrose density gradient ( Figure 3-figure supplement 1D-F). Thus, we hypothesized that RPL3 methylation may impact protein synthesis. To understand the potential role of methylation in RPL3, we reanalyzed published cryo-EM data (Osterman et al., 2020) and assessed the τ-N-methyl moiety on His245 of RPL3 ( Figure 3A), which indicated that τ-Nmethylated RPL3 is a stoichiometric component of the ribosome. A similar density of methylation on the histidine of RPL3 has also been found in rabbit ribosomes (Bhatt et al., 2021). On the other hand, the ribosomes isolated from METTL18 KO cells lost density at the τ-N position of the His245 ( Figure 3B, Figure 3-figure supplement 2, Table 1). The absence of methylation at the τ-N position allowed nitrogen to form hydrogen bonds with G1595 of 28S rRNA ( Figure 3B). Given that G1595 is located in the loop of helix 35, which macrolide antibiotics target in bacterial systems (Kannan and Mankin, 2011), this difference in the interaction between His245 and G1595 suggests an alteration in the translation reaction.      Nonetheless, we investigated the implications of RPL3 methylation defects across the transcriptome by ribosome profiling (Ingolia et al., 2009;Iwasaki and Ingolia, 2017). Strikingly, we found increased translation elongation of Tyr codons in METTL18 KO cells; ribosome occupancy on Tyr codons at the A-site was selectively reduced in the mutant cells ( Figure 4A and B). This trend in ribosome occupancy was not observed at the P and E sites (Figure 4-figure supplement 2A and B). To evaluate the amino acid context associated with the high elongation rate, we surveyed the motifs around the A-site with reduced ribosome    Figure 4C) and analyzed the enriched/depleted sequence in the group ( Figure 4D). Remarkably, Tyr at the A-site was the predominant determinant for fast elongation in METTL18 KO cells ( Figure 4D). The smoother elongation may be caused by increased tRNA abundance. However, tRNA Tyr GUA , which decodes both UAU and UAC codons, was noticeably reduced by METTL18 depletion ( Further ribosome profiling data analysis supported that the accommodation of tRNA at the A-site may not explain the modulation of elongation by RPL3 methylation. Ribosome footprints possess two distinct populations of different lengths (short, peaked at ~22 nt; long, peaked at ~29 nt), reflecting the presence of A-site tRNA (Lareau et al., 2014;Wu et al., 2019; Figure 4E). Since A-site tRNAfree ribosomes are more susceptible to RNase treatment at the 3′ end, the trimmed short footprints represent nonrotated ribosomes waiting for A-site codon decoding by tRNA. On the other hand, long footprints originate from ribosomes accommodated with A-site tRNA in the middle of the peptidyl transfer reaction or subsequent subunit rotation (Lareau et al., 2014;Wu et al., 2019). The reduced footprints on Tyr codons in METTL18 KO cells were more prominent in long footprints than short footprints ( Figure 4F). Moreover, the long footprints were recovered by ectopic expression of METTL18 protein ( Figure 4G). These data suggested that the process or processes downstream of codon decoding are promoted in KO cells. This observation was reasonable, given the relatively long distance between the τ-N-methylated histidine and the mRNA codon.
To test the cell-type specificity, we further extended our ribosome profiling experiments in HAP1 cells, which originate from chronic myelogenous leukemia. We investigated ribosome footprints on the Tyr codons in three independent METTL18 KO cell lines (1-nt, 2-nt, and 4-nt deletions) that should lead to truncated proteins (Figure 4-figure supplement 2G) and observed the reduction of ribosome occupancies on the codons in those cell lines as well ( Figure 4H). These data suggested consistent effects of RPL3 methylation on elongation irrespective of cell type.

Ribosomes deficient for RPL3 methylation exhibit higher processivity on Tyr codons in vitro
To further assess the effect of RPL3 methylation on Tyr codon elongation, we combined hybrid in vitro translation (Erales et al., 2017;Panthu et al., 2015) with the Renilla-firefly luciferase fusion reporter system (Kisly et al., 2021; Figure 5A). In this setup, we purified ribosomes from HEK293T (naïve or METTL18 KO) cells, added them to ribosome-depleted rabbit reticulocyte lysate (RRL), and then conducted an in vitro translation assay (i.e., hybrid translation) (Erales et al., 2017;Panthu et al., 2015; Figure 5A). Indeed, we observed that removal of the ribosomes from RRL decreased protein synthesis in vitro and that complementation with ribosomes from HEK293T cells recovered the activity ( Figure 5-figure supplement 1A).
To test the effect on Tyr codon elongation, we harnessed the fusion of Renilla and firefly luciferases; this system makes it possible to detect the delay/promotion of downstream firefly luciferase synthesis compared to upstream Renilla luciferase and thus to focus on the effect of the sequence inserted between the two luciferases on elongation (Kisly et al., 2021; Figure 5A). For better detection of the       effects on Tyr codons, we used a repeat of the codon (×39; the number was due to cloning constraints). We note that the insertion of Tyr codon repeats reduced the elongation rate (or processivity), as we observed the reduced slope of the downstream Fluc synthesis ( Figure 5-figure supplement 1B).
Then, we coupled the in vitro translation system and the reporter. We observed that RPL3 methylation-deficient ribosomes exhibited faster elongation on Tyr repeats than ones from naïve cells ( Figure 5B).
These in cell and in vitro data together indicated that RPL3 methylation mediated a slowing of translation elongation on the Tyr codons.

RPL3 histidine methylation ensures the proper proteostasis
Ribosome traverse along the mRNA determines the quality of protein synthesized (Cassaignau et al., 2020;Collart and Weiss, 2019;Stein and Frydman, 2019). Slowdown of ribosome elongation is advantageous since it allows the duration of nascent protein folding before completion of protein synthesis. Therefore, we reasoned that translation elongation slowdown at Tyr codons by RPL3 methylation facilitates protein folding on ribosomes and maintains proper homeostasis of the proteome.
To test this possibility, we employed an aggregation-prone firefly luciferase (Fluc) reporter (Arg188Gln-Arg261Gln double mutant or DM) fused to enhanced green fluorescent protein (EGFP) (Gupta et al., 2011). Since this engineered protein necessitates chaperones to fold properly, the reduced pool of available chaperones (i.e., proteotoxicity) leads to aggregation puncta of the reporter protein in cells. Indeed, METTL18 depletion induced the aggregation of FlucDM but not Fluc WT reporter ( Figure 6A and B). As shown by the recovery of protein abundance by treatment with the proteasome inhibitor MG132 ( Figure 6C), FlucDM protein was synthesized in METTL18 KO cells of low quality and subjected to degradation.
Then, we explored the proteome, the quality of which was assisted by RPL3 histidine methylation. For this purpose, we surveyed the proteins aggregated in METTL18 KO cells by SILAC ( Figure 7A). We observed that a subset of proteins were enriched in precipitates of METTL18 KO cell lysates ( Figure 7B). This subgroup significantly accumulated Tyr-rich proteins (defined as proteins possessing The online version of this article includes the following source data and figure supplement(s) for figure 5: Source data 1. Primary data for graphs in Figure 5B.  30 Tyr or more) (hypergeometric test, p=0.0068) ( Figure 7B). The high probability of protein precipitates could not be explained by the increased net protein synthesis measured by ribosome profiling (Figure 7-figure supplement 1A). More generally, Tyr-rich proteins were more prone to precipitate upon the deletion of METTL18 (Figure 7-figure supplement 1B) than proteins rich in other amino acids ( Figure 7C). Thus, proteomic analysis of cellular precipitates revealed that the modulation of Tyr-specific translation elongation by RPL3 methylation confers proteome integrity. These data led us to further investigate the properties of the proteome associated with Tyr. Here, we surveyed the aggregation propensity of the precipitated proteins by TANGO, which is based on statistical mechanics (Fernandez-Escamilla et al., 2004). Strikingly, metagene analysis showed prominent enrichment of the TANGO-predicted aggregation propensity around the Tyr codons ( Figure 7D). As exemplified in the MACROH2A1 protein, the subpart of the aggregation-prone region in this protein was found on Tyr with reduced ribosome occupancies in METTL18 KO cells ( Figure 7E Ultimately, the low-quality protein synthesized by RPL3-unmethylated ribosomes may serve as a substrate for proteasomes. To assess the fraction of proteins degraded by proteasome, we conducted SILAC analysis of the total proteome in METTL18 KO cells treated with MG132, a proteasome inhibitor ( Figure 8A). Indeed, this approach revealed a subset of more efficiently degraded proteins in METTL18 KO cells ( Figure 8B); this group of proteins tended to be reduced in METTL18 KO cells and recovered by MG132 treatment. Moreover, this subset of proteins included Tyr-rich proteins ( Figure 8C), which was congruent with the enhanced elongation observed in ribosome profiling.
The relationships among the aggregation-prone character of the protein, the cellular protein precipitates, increased proteasomal substrates, and reduced ribosome occupancy indicates that Tyr translation modulated by RPL3-methylated ribosomes is associated with the quality of the synthesized proteins, preventing unwanted protein aggregation ( Figure 9). The online version of this article includes the following source data for figure 6: Source data 1. Full and unedited images corresponding to Figure 6A.
Source data 2. Full and unedited blots corresponding to Figure 6C.
Source data 3. Primary data for graphs in Figure 6B.

Discussion
In addition to SETD3 Guo et al., 2019;Kwiatkowski et al., 2018;Wilkinson et al., 2019;Zheng et al., 2020), METTL18 provides a second example of τ-N-methyltransferase. Whereas τ-N-methylation at the equivalent residue (His243) in yeast Rpl3 has been indirectly demonstrated (Webb et al., 2010), this study provided solid evidence (such as MS and cryo-EM) of the modification on the homolog in humans. Similar to prior yeast work (Al-Hadid et al., 2014), human RPL3 alone could not be methylated by METTL18. Rather, RPL3 was most likely to be modified in the early 60S biogenesis intermediate complex. This suggests that METTL18 recognizes a unique interface formed by RPL3 and other ribosome proteins and/or assembly factors. In the recent structural studies on pre-60 assembly intermediates (Kater et al., 2017;Sanghai et al., 2018), His245 of RPL3 in the early pre-60S in state B (Kater et al., 2017) is exposed to solvent (Figure 9-figure supplement 1A), possibly enabling access to METTL18, although His245 per se was not visible in the structure because of flexibility. In contrast, ribosomal proteins and rRNAs in the later stage of 60S biogenesis (at state D) (Kater et al., 2017) fill the corresponding space ( Figure 9-figure supplement 1B). Thus, histidine methylation by METTL18 should be restricted to specific timing of the macromolecule assembly.
In the course of this work, a paper from Falnes and coworkers was published and reached a similar conclusion regarding the methylation site (His245 in RPL3) and the methylation type (τ-N position) mediated by human METTL18 . Although the earlier report showed that recombinant METTL18 protein methylated isolated ribosomes from METTL18 KO, the authors also observed that METTL18 localized in nucleoli  where ribosomes are still under assembly. These data could be interpreted to show that the purified ribosome may consist of contaminated pre-60S, and this fraction was an efficient substrate of METTL18.
The impact of METTL18 loss on translation found in this study differed from that in the earlier report . In the earlier report, ribosome profiling in METTL18 KO HAP1 cells revealed widespread effects of translation elongation, exemplified by slowdown of the GAA codon . In contrast, the same experiment in this work with HEK293T and HAP1 (including the same cell line [2-nt del.] used in Małecki et al., 2021) showed that METTL18 KO enhanced ribosome traversal on Tyr codons (Figure 4). We did not have any information on how to reconcile this inconsistency in ribosome profiling data. At least, as reported previously , we have made a similar observation in the bulk ribosomal complex abundance in the METTL18 KO HAP1 cell line (2-nt del.); reduced polysomes ( Figure 9-figure supplement 2A and B) and unaltered 40S and 60S (Figure 9-figure supplement 2C-E). The effect of RPL3 methylation on translation elongation could be dynamic and dependent on cellular status affected by circumstances (e.g., culturing conditions). Future studies across diverse tissues and cellar status will provide a global look at the conditiondependent effects of the ribosome protein methylation.
The modification-mediated ribosome slowdown revealed in this study provides a unique example of translational control since modification in general often offers a smooth translation, as exemplified in tRNA modifications (Nedialkova and Leidel, 2015;Tuorto et al., 2018). The exact mechanism of how His245 methylation in RPL3 leads to Tyr-specific elongation retardation remains elusive. In bacteria, the loop of helix 35, where unmethylated His245 interacts, was heavily modified (Kannan and Mankin, 2011), although the role of rRNA modification has been unclear. Eukaryotic RPL3 may functionally replace RNA modification by histidine methylation. From another viewpoint, His245 is located in the 'basic thumb' region (Arg234-Arg246), which bridges the interaction of 28S rRNA helices (H61, H73, and H90) and facilitates the formation of a so-called 'aminoacyl-tRNA accommodation corridor' (Meskauskas and Dinman, 2010). Thus, the methylation of His245 may allosterically alter the dynamic character of the aminoacyl-tRNA accommodation corridor to restrict the movement of charged Tyr on tRNA. Indeed, conformational changes in the aminoacyl-tRNA accommodation corridor were suggested by molecular dynamics simulation (Gulay et al., 2017).   We also did not exclude the possibility that this modification may impact other processes of translation. Indeed, an earlier report in yeast suggested that Hpm1 (a homolog of METTL18) deletion decreased the fidelity of translation, inducing stop codon readthrough (Al-Hadid et al., 2016;Al-Hadid et al., 2014). However, our ribosome profiling data in HEK293T cells did not show any increase in ribosome footprints in the 3′ UTR (Figure 9-figure supplement 1C and D) that could be accumulated by the stop codon readthrough (Arribere et al., 2016;Dunn et al., 2013).
Although ribosome traversal along the CDS is generally defined by the decoding rate in bacteria (Mohammad et al., 2019) and yeasts (Hussmann et al., 2015;Wu et al., 2019), the codon/amino acid-specific effects of RPL3 histidine methylation in humans suggest that the landscape is more complex in higher eukaryotes. Indeed, ribosome occupancy in mammals is poorly predicted by tRNA abundance in cells (Han et al., 2020). Thus, it is not surprising that a wide array of ribosome modifications, including RPL3 histidine modification, ultimately define the speed of ribosome movement and thus the quality of protein synthesized in cells.

pET19b-mMETTL18
To express N-terminally His-tagged full-length mouse METTL18, cDNA was PCR-amplified from a FANTOM clone (AK139786) and cloned into NdeI and XhoI sites of the pET19b vector (Novagen).

pCold-GST-mMETTL18
To express N-terminally His-and GST-tagged full-length mouse METTL18, the PCR-amplified fragment was cloned into the NdeI and XhoI sites of the pCold-GST vector (TaKaRa).
pcDNA3-hRPL3-FLAG (WT and His245Ala) and pcDNA3-mRPL3-FLAG (WT and His245Ala) To express C-terminally FLAG-tagged mouse and human RPL3, each cDNA fragment was amplified from the mouse cDNA and HEK293T cDNA libraries and cloned into EcoRI and NotI sites of the pcDNA3 vector (Invitrogen) with a C-terminal FLAG-tag sequence. To generate His245Ala mutants, the QuikChange Site-Directed Mutagenesis Kit (Agilent Technologies) was used.

psiCHECK2-Y0× and Y39×
To generate the psiCHECK2-Y0× reporter, the intergenic region between Rluc and Fluc was excluded by inverse PCR. The plasmid encodes the ORF for the Rluc-Fluc fusion. To generate the psiCHECK2-Y39× reporter, 39 repeats of the TAC sequence were inserted between Rluc and Fluc of psiCHECK2-Y0×.

Cell lines: HEK293T
HEK293T KO cell lines were generated by the CRISPR-Cas9 system. All cell lines in the laboratory were routinely tested for Mycoplasma contamination with the MycoAlert Mycoplasma Detection Kit (LONZA) and confirmed negative.

METTL18 KO cells with stable METTL18 expression
Retrovirus packaging cells were transfected with pQCXIP-hMETTL18-HA, pQCXIP-hMETTL18-Asp193Lys-Gly195Arg-Gly197Arg-HA, or the pQCXIP empty vector (as a negative control) using PEI transfection reagent (Polysciences) and cultured for 24 hr. Then, METTL18 KO cells were inoculated with the virus-containing culture supernatant and 4 μg/ml of polybrene. At 24 hr post-infection, cells were selected with 1 μg/ml puromycin and cultured for additional 2 weeks. e-Myco VALiD (LiliF) confirmed that the cells were negative for Mycoplasma.

SETD3 KO and SETD3-METTL18 DKO cells
pL-CRISPR.EFS.tRFP-gSETD3, which expressed a guide RNA designed to induce small insertion or deletion (InDel), was transfected into HEK293T cells or METTL18 KO cells. After 2 days of incubation, individual RFP-positive cells were sorted into 96-well plates. The clonal cell lines were further screened by Western blot for SETD3 protein.

Mass spectrometry Multiple reaction monitoring
Methylhistidine content analysis was performed essentially as previously described . Proteins were precipitated with acetone and hydrolyzed to amino acids with 6 N HCl at 110°C for 24 hr. After dissolving in 25 µl of 5 mM ammonium formate/0.001% formic acid, the amino acids were applied to a LC system (Thermo Fisher Scientific, Vanquish UHPLC). The amino acids loaded on a C18 column (YMC, YMC-Triart C18, 2.0 × 100 mm length, 1.9 µm particle size) were separated at a flow rate of 0.3 ml/min by gradient elution of mobile phase 'A' (5 mM ammonium formate with 0.001% formic acid) and mobile phase 'B' (acetonitrile) as follows: 0/0 -1.5/0 -2/95 -4/95 -4.1/0 -7/0 (min/%B). The effluent was then directed to an electrospray ion source (Thermo Fisher Scientific, HESI-II) connected to a triple quadrupole mass spectrometer (Thermo Fisher Scientific, TSQ Vantage EMR) in positive ion MRM mode. The electrospray was run with the following settings: spray voltage of 3000 V, vaporizer temperature of 450°C, sheath gas pressure of 50 arbitrary units, auxiliary gas pressure of 15 arbitrary units, and collision gas pressure of 1.0 mTorr. The transition of specific MH+→ fragment ions was monitored (His,m/z 156.1→83.3,93.2,and 110.2;m/z 170.1→95.3,97.3,and 109.2;m/z 170.1→81.3,83.3,and 124.2). Data were calibrated with 1-250 nM standards (His, π-N-MeHis, and τ-N-MeHis) at every run. The concentrations of His, π-N-MeHis, and τ-N-MeHis in the samples were calculated from the calibration curves obtained from the standards.

ProSeAM-SILAC-MS
ProSeAM was synthesized as previously described (Sohtome et al., 2018). ProSeAM substrate screening was carried out as reported  with some modifications. METTL18 KO cells were cultured in Dulbecco's modified Eagle's medium (DMEM) containing either light Arg/ Lys or heavy isotope-labeled Arg ( 13 C 6 15 N 4 l-arginine)/Lys ( 13 C 6 15 N 2 l-lysine) (Thermo Fisher Scientific, respectively) at least six doubling times. The cells were lysed with 50 mM Tris-HCl pH 8.0, 50 mM KCl, 10% glycerol, and 1% n-dodecyl-βd-maltoside. For the cells cultured with the heavy amino acids, the lysate containing 200 μg of proteins was incubated with 150 μM ProSeAM and 10 μg of His-METTL18 in 50 mM Tris-HCl pH 8.0 at 20°C for 2 hr. For the lysate with the light amino acids, His-METTL18 was omitted from the reaction. The reaction was stopped by the addition of four volumes of icecold acetone. The proteins were precipitated by centrifugation at 15,000 × g for 5 min, washed once with ice-cold acetone, and then dissolved in 58.5 µl of 1× PBS containing 0.2% sodium dodecyl sulfate (SDS). After the addition of 15 µl of 5× click reaction buffer (7.5 mM sodium ascorbate [Nacalai Tesque], 0.5 mM TBTA [AnaSpec], and 5 mM CuSO 4 ) and 1.5 µl of 10 mM Azide-PEG4-Biotin (Click Chemistry Tools), the click reaction was conducted for 60 min at room temperature, stopped with four volumes of ice-cold acetone, and precipitated as described above. The protein in the pellet was resuspended in 75 µl of binding buffer (1× PBS, 0.1% Tween-20, 2% SDS, and 20 mM DTT) and sonicated for 10 s. The light and heavy isotope-labeled samples were pooled in 450 µl of IP buffer (Tris-buffered saline [TBS] and 0.1% Tween-20) containing 3 µg of Dynabeads M-280 Streptavidin (Thermo Fisher Scientific) and incubated for 30 min at room temperature (note that the final SDS concentration in the solution was 0.5%). The protein-bound beads were washed three times with bead wash buffer (1× PBS, 0.1% Tween-20, and 0.5% SDS) and twice with 100 mM ammonium bicarbonate (ABC) and then used for Western blotting and MS.
For MS/MS analysis, the beads were incubated in 20 mM DTT and 100 mM ABC for 30 min at 56°C and then for 30 min at 37°C in the dark with supplementation with 30 mM iodoacetamide. Subsequently, proteins were digested with 1 µg trypsin (Promega) and subjected to LC (Thermo Fisher Scientific, EASY-nLC 1000) coupled to a Q Exactive Hybrid Quadrupole-Orbitrap Mass Spectrometer (Thermo Fisher Scientific) with a nanospray ion source in positive mode, as previously reported . The peptides loaded on a NANO-HPLC C18 capillary column (0.075 mm inner diameter × 150 mm length, 3 µm particle size, Nikkyo Technos) were eluted at a flow rate of 300 nl/min with the two different slopes of mobile phase 'A' (water with 0.1% formic acid) and mobile phase 'B' (acetonitrile with 0.1% formic acid): 0-30% of phase B in 100 min and 30-65% of phase B in 20 min. Subsequently, the mass spectrometer in the top 10 data-dependent scan mode was run with the following parameters: spray voltage, 2.3 kV; capillary temperature, 275°C; mass-to-charge ratio, 350-1800; normalized collision energy, 28%. The MS and MS/MS data obtained with Xcalibur software (Thermo Fisher Scientific) were surveyed in the Swiss-Prot database with Proteome Discoverer (version 2.3, Thermo Fisher Scientific) and MASCOT search engine software (version 2.7, Matrix Science). Peptides with false discovery rates (FDRs) less than 1% were considered. Proteins with the following criteria were defined as METTL18-dependent labeled proteins: 1.5-fold or more increase in heavy amino acid sample compared to light amino acid sample; one, 10% or more coverage of the protein; and three or more peptides identified.

LC-MS/MS for methylated peptide
The SDS-PAGE-separated and Coomassie staining-visualized proteins were excised and destained. The gel slices were reduced with 50 mM DTT and 4 M guanidine-HCl at 37°C for 2 hr, followed by alkylation with 100 mM acrylamide at 25°C for 30 min. The RPL3 proteins were digested with chymotrypsin. The MS and MS/MS spectra were acquired with a Q Exactive HFX (Thermo Fisher Scientific). The mass spectrometer was operated in positive mode. The MS/MS spectra were obtained using a data-dependent top 10 method. The acquired data were processed using Proteome Discoverer (version 2.3, Thermo Fisher Scientific). The processed data were used to search with MASCOT (version 2.7, Matrix Science) against the in-house database including the amino acid sequences of RPL3 using the following parameters: type of search, MS/MS ion search; enzyme, none; fixed modification, none; variable modifications, Gln->pyro-Glu (N-term Q), oxidation (M), oropionamide (C), and methyl (H); mass values, monoisotopic; peptide mass tolerance, ±15 ppm; fragment mass tolerance, ±30 mmu; peptide charge, 1+, 2+, and 3+; instrument type, ESI-TRAP.
After a brief wash with PBS, cells were lysed with buffer containing 20 mM Tris-Cl pH 7.5, 150 mM KCl, 5 mM MgCl 2 , 1% Triton X-100, and 1 mM DTT. The protein concentration was measured using Qubit 2.0 Fluorometer (Thermo Fisher Scientific). The same amounts of proteins from light and heavy isotope-labeled lysates were mixed and centrifuged at 500 × g for 3 min. The supernatant was further centrifuged at 20,000 × g and 4°C for 15 min. The precipitate was collected and used for analysis.
Filter-aided sample preparation (FASP) was used for protein digestion (Wiśniewski et al., 2009). The precipitate was dissolved in SDT lysis buffer (4% [w/v] SDS, 0.1 M DTT, and 100 mM Tris-HCl pH 7.6) and incubated at 95°C for 5 min. Denatured samples were diluted 10 times with UA buffer (8 M urea and 100 mM Tris-HCl pH 8.5) and loaded to Vivacon 500, 30000 MWCO Hydrosart (Sartorius) to trap the protein on the filter. The filter unit was washed with the UA buffer. Proteins on the filter unit were alkylated with 100 μl of the IAA solution (0.05 M iodoacetamide in UA). Then, the filter unit was washed with 100 μl of UA buffer three times and 100 μl of 50 mM NH 4 HCO 3 three times. Proteins on the filter unit were digested with 40 μl of trypsin solution (trypsin [V5111, Promega] in 50 mM NH 4 HCO 3 ) at 37°C for 18 hr. Then, the peptides were eluted from the filter unit by 40 μl of NH 4 HCO 3 twice and 50 μl of 0.5 M NaCl once and then pooled.
LC-MS/MS analysis was performed using EASY-nLC 1000 (Thermo Fisher Scientific) and Q Exactive (Thermo Fisher Scientific) equipped with a nanospray ion source. The peptides were separated with a NANO-HPLC capillary column C18 (0.075 × 150 mm, 3 μm, Nikkyo Technos) at 300 nl/min flow rate with strep gradients of solvent A (0.1% formic acid) and solvent B (acetonitrile with 0.1% formic acid); 0-30% B for 100 min and then 30-65% B for 20 min. The resulting MS and MS/MS data were searched against the Swiss-Prot database using Proteome Discoverer (version 2.4, Thermo Fisher Scientific) with MASCOT search engine software (version 2.7, Matrix Science). The peptides with FDR values of 0.05 or less were considered for the subsequent analysis. To quantify the difference of peptides labeled with differential isotopes, the built-in SILAC 2-plex quantification method in Proteome Discoverer (version 2.4, Thermo Fisher Scientific) was used. Peptide abundances were normalized by total peptide amount. p-Values were calculated by the background-based t-test and then adjusted by the Benjamini-Hochberg method.
For total proteome analysis, we treated cells with 0.25 μM MG132 (FUJIFILM Wako Chemicals) for 24 hr before cell harvest. Cell lysates were prepared as described above, and the supernatant obtained by centrifugation at 20,000 × g and 4°C for 15 min was used for the downstream analysis.

Methylation assay
FLAG-tagged RPL3 was transiently expressed in METTL18 KO cells and immunopurified with ANTI-FLAG M2 Affinity Gel (Sigma-Aldrich). The purified proteins were incubated in 1× reaction buffer (50 mM Tris-HCl pH 8.5 and 50 mM MgCl 2 ) with 1 µg of His-GST-METTL18, 2 µM MTAN, and 0.01 µCi of 14 C-labeled SAM (PerkinElmer) at 30°C for 2 hr. The reaction was stopped by the addition of Laemmli SDS-sample buffer. Proteins were separated on a 10% acrylamide SDS-PAGE gel. The dried gel was exposed to an imaging plate (FUJIFILM) for 48 hr. The autoradiograph was detected with a phosphor imaging scanner (Cytiva, Amersham Typhoon).

Cryo-EM
The crude ribosomal pellet was suspended in buffer A (50 mM Tris-HCl pH 7.5, 150 mM KCl, 4 mM magnesium acetate, 1 mM DTT, 7% [w/v] sucrose, and 1 mM puromycin) by mixing with a magnetic stirrer for 4 hr on ice. After stirring, the suspension was centrifuged at 15,000 × g for 10 min at 4°C. The supernatant was loaded onto a HiPrep 16/60 Sephacryl S-500 column (Cytiva) equilibrated with buffer A without puromycin. The fraction was recovered and concentrated using Amicon Ultra (MWCO 50 kDa, Merck Millipore). The concentrated mixture was supplemented with 0.1 mM puromycin, 2 mM magnesium acetate, and 2 mM ATP and incubated for 30 min at 37°C. The reaction was loaded onto a 10-40% (w/v) sucrose gradient with buffer B (50 mM Tris-HCl pH 7.5, 500 mM KCl, 4 mM magnesium acetate, and 2 mM DTT) and centrifuged at 25,000 rpm in an SW28 rotor for 16 hr at 4°C. 2 ml fractions were successively fractionated from the top of the gradient. An aliquot of each fraction was analyzed by SDS-PAGE, and the gels were stained with Coomassie brilliant blue (CBB) to detect the 40S and 60S subunit proteins. The 40S-and 60S-subunit fractions were mixed and concentrated using Amicon Ultra filter units (MWCO 50 kDa, Merck Millipore). The concentrated mixture was loaded onto a 10-50% (w/v) sucrose gradient with buffer C (50 mM Tris-HCl pH 7.5, 150 mM KCl, 10 mM magnesium acetate, and 2 mM DTT) and centrifuged at 28,000 rpm in an SW41Ti rotor for 3 hr at 4°C. Gradient fractionation was carried out using a piston gradient fractionator equipped with a TRIAX flow cell detector (BioComp) by continuous monitoring of absorbance at a wavelength of 280 nm. The fractions containing 80S ribosomes were dialyzed against preparation buffer (10 mM HEPES-KOH pH 7.5, 30 mM potassium acetate, 10 mM magnesium acetate, and 1 mM DTT) and concentrated using Amicon Ultra filter units (MWCO 50 kDa, Merck Millipore). The concentrated sample was quantified by measuring absorbance at a wavelength of 260 nm and flash-cooled with liquid nitrogen.
For cryo-EM sample preparation, Quantifoil R1.2/1.3 300 mesh copper grids (Quantifoil) were covered with an amorphous carbon layer prepared in-house. The thawed sample was diluted to 70 nM (an absorbance at 260 nm of 3.5) with preparation buffer, and 3 μl of the sample was applied onto grids at 4°C at 100% relative humidity using a Vitrobot Mark IV (FEI). After incubation for 30 s and blotting for 3 s, the grids were plunged into liquid ethane.
The cryo-EM dataset was collected with a Tecnai Arctica transmission electron microscope (FEI) operated at 200 kV using a K2 summit direct electron detector (Gatan) (0.97 Å/pixel). The 5517 images collected were fractionated to 40 frames, with a total dose of ~50 e -/Å 2 .
Processing of cryo-EM data was performed with RELION-3.1 (Zivanov et al., 2020). The movie frames were aligned with MotionCor2 (RELION's own implementation), and the CTF parameters were estimated with CTFFIND-4.1 (Rohou and Grigorieff, 2015). Particles were automatically picked using a template-free Laplacian-of-Gaussian (LoG) filter (250-500 Å), and 381,227 particles were extracted with twofold binning. After 2D classification, 136,688 particles were selected and applied to 3D classification. A low-pass-filtered (40 Å) map of the human 80S ribosome (EMD-9701) (Yokoyama et al., 2019) was used as a reference map for 3D classification, and 118,470 particles were selected after this step. These particles were re-extracted without rescaling and used in 3D refinement, Bayesian polishing, CTF refinement, and then 3D refinement again. After these steps, focused refinement with a mask on the 60S subunit and postprocessing resulted in a resolution of 2.72 Å.
For molecular modeling, the model of the 60S subunit from the human 80S ribosome structure at 2.9 Å resolution (PDB: 6QZP) (Natchiar et al., 2017) was used as a starting model and manually fitted into the map using UCSF Chimera (Pettersen et al., 2004). Map sharpening and model refinement were performed in PHENIX (Adams et al., 2010), and the model was further refined manually with Coot (Emsley et al., 2010). The modified nucleotides of ribosomal RNAs were introduced based on quantitative MS data (Taoka et al., 2018).
To knock down RPL17, HEK293T cells were seeded in complete growth medium in 10 cm 2 dishes 24 hr before siRNA transfection. Then, the cells were transfected with RPL17 siRNA (ON-TARGETplus Human RPL17 siRNA, L-013633-01-0005, Horizon Discovery) or control siRNA (ON-TARGETplus Nontargeting Control Pool, D-001810-10-50, Horizon Discovery) by TransIT-X2 Dynamic Delivery System (Mirus) according to the manufacturer's instructions. After 72 hr of siRNA transfection, cells were lysed by the procedure described above.
The gradients were fractionated with continuous measurement of the absorbance at 260 nm by a Triax Flow Cell (BioComp) and Micro collector (ATTO). For ribosomal complex quantification, the straight line connecting the valleys before and after peaks was defined as a background baseline. Then, the area enclosed by the baseline and the peak waveform was calculated. For Western blot ( Figure 2B) or MS analysis (Figure 1-figure supplement 2B), fractions were concentrated using Amicon Ultra filter units (MWCO 10 kDa, Millipore).

Newly synthesized protein labeling by OP-puro
Metabolic labeling of nascent proteins with OP-puro was performed as previously described . Cells were treated with 20 µM OP-puro and incubated at 37°C for 30 min in a CO 2 incubator. After washing with PBS, cells were lysed with buffer containing 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl 2 , and 1% Triton X-100. Nascent polypeptides were labeled with IRdye800CW Azide (LI-COR Biosciences) with a Click-iT Cell Reaction Buffer Kit (Thermo Fisher Scientific). After free dye was removed by a G-25 column (Cytiva), labeled polypeptides were separated by SDS-PAGE. The gel was imaged by Odyssey CLx (LI-COR Biosciences) for the detection of nascent peptides with infrared at 800 nm. Then, total proteins were stained with CBB (FUJIFILM Wako Chemicals) and imaged with an infrared 700 nm signal. The gel area ranging from 17 kDa to 280 kDa was quantified using Image Studio (version 5.2, LI-COR Biosciences), and the nascent peptide signal was normalized to the total protein signal.
Cell lysates were treated with RNase I, and 17-34-nt protected RNA fragments were gel-excised. After the RNA fragments were ligated with preadenylated linkers, ribosomal RNAs were removed by a Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina, RZG1224). Then, the ligated RNA fragments were reverse-transcribed. The cDNAs were circularized using CircLigaseII (Lucigen) and PCR-amplified. The libraries were sequenced on a HiSeq4000 (Illumina, single reads for 50 nt) for HEK293T cells and a HiSeqX Ten (Illumina, paired ends for 150 nt) for HAP1 cells.

Data analysis
After removal of the linker sequences, all reads were aligned to human noncoding RNAs (including rRNA, tRNA, snoRNA, snRNA, and microRNA) using STAR (version 2.7.0a) (Dobin et al., 2013). Then, the remaining reads were aligned to the human hg38 reference genome by STAR and assigned to canonical transcripts in the University of California, Santa Cruz (UCSC), known gene reference. For HAP1 cell data, the sequences of reads 1 were corrected by reads 2, before quality filtering and adapter sequence trimming.
The A-site offsets for each footprint length were empirically estimated: in the dataset with naïve and METTL18 KO HEK293T cells, 15 for 20-22, 24, and 28-30-nt-long footprints and 16 for 23 and 32-33-nt-long footprints; in the dataset with METTL18 KO HEK293T cells with METTL18 WT and empty vector expression, 15 for 28-31-nt-long footprints and 16 for 32-33-nt-long footprints; and in the dataset with naïve and METTL18 KO HAP1 cells, 15 for 28-33-nt-long footprints. The reads of each codon were normalized by the average reads per codon of the transcript. We excluded the first and last 5 codons from the analysis. Transcripts with an average reads per codon of 0.3 or higher were considered. The value of ribosome occupancy was the average of normalized reads at each position.
To search for motifs associated with Tyr codon around A-site, ribosome occupancies on the seven amino acid motifs were averaged. Motifs with average ribosome occupancy scores greater than 0.3 were used for the downstream analysis. Then, the log 2 -fold changes in METTL18 KO cells over naïve cells were calculated. Motifs with log 2 -fold changes less than mean -2 SD were subjected to kpLogo (http://kplogo.wi.mit.edu) (Wu and Bartel, 2017).

Hybrid in vitro translation
The hybrid translation assay was performed as described previously (Erales et al., 2017;Panthu et al., 2015) with optimization for the purpose of this study.
The DNA fragments were used for in vitro transcription by T7-Scribe Standard RNA IVT kit (CELLSCRIPT). Then, the RNAs were capped with the ScriptCap m 7 G Capping system (CELLSCRIPT) and polyadenylated with the A-Plus poly(A) polymerase Tailing Kit (CELLSCRIPT).

Ribosome preparation
After brief washing with PBS, cells were resuspended with PBS and centrifuged at 500 × g for 3 min. The pellet of cells was resuspended in the same volume of buffer R (10 mM HEPES pH 7.5, 10 mM KOAc, 1 mM MgOAc 2 , and 1 mM DTT) and incubated for 15 min on ice. Subsequently, the mixture was vortexed for 30 s and centrifuged at 16,000 × g for 10 min at 4°C. Then, 300 μl of the supernatant was ultracentrifuged through a 1 ml sucrose cushion (1 M sucrose in buffer R) at 240,000 × g for 2 hr 15 min at 4°C by an Optima MAX-TL ultracentrifuge (Beckman Coulter) with a TLA110 rotor (Beckman Coulter). The pellet was rinsed with buffer R2 (20 mM HEPES pH 7.5, 10 mM NaCl, 25 mM KCl, 1.1 mM MgCl 2 , and 7 mM 2-mercaptoethanol) and then resuspended in 30 μl of buffer R2 by stirring at 4°C for 15 min, flash-frozen by liquid nitrogen, and stored at −80°C. The ribosome concentration was determined by the absorbance at 260 nm using a NanoDrop (Thermo Fisher Scientific).

Translation reaction
In vitro translation was typically performed in a 10 μl reaction mixture containing 5 μl of RRL supernatant, 22.6 nM of purified ribosome, 1.1 nM of reporter mRNA, 75 mM KCl, 0.75 mM MgCl 2 , and 20 µM of amino acid mixture (Promega).
For the Fluc reporter, the reaction mixture was incubated at room temperature for 90 min and stopped by the addition of 20 μl of 1× Passive Lysis Buffer (Promega). The FLuc luminescence from 30 μl of the mixture was measured with the Dual-Luciferase Reporter Assay System (Promega).
For Rluc-Y0×-Fluc and Rluc-Y39×-Fluc reporters, the reaction mixture above was scaled up to 120 μl and incubated at room temperature. 10 μl of the reaction mixture was taken as an aliquot every 5 min and mixed with 20 μl of 1× Passive Lysis Buffer (Promega) to stop the reaction. The Rluc and FLuc luminescence from 30 μl of the mixture was measured with the Dual-Luciferase Reporter Assay System (Promega). The luminescences at 20-30 min were used to calculate the slope of Rluc and Fluc synthesis.
To count the aggregation foci, 2 × 10 5 cells were seeded in 35-mm glass-bottom dishes (IWAKI) and cultured for 24 hr. Cells were transfected with 2 µg of pCI-neo Fluc-EGFP or pCI-neo FlucDM-EGFP and 4 µg of PEI (Polysciences) and cultured for an additional 24 hr. GFP fluorescence was observed under an FLUOVIEW FV3000 (Olympus). At least 100 GFP-positive cells were observed to count cells with aggregates (n = 3).
For MG132 treatment, cells were treated with 0.25 µM MG132 at 24 hr post transfection. After subsequent 24 hr culture, cells were harvested as described in the 'Ribosome profiling' section.

Assessment of expression levels of ribosomal RNAs
300 ng of total RNA purified from cell lysates prepared as described in 'Ribosome profiling' section was analyzed with a microchip electrophoresis system (MultiNA, Shimadzu).  The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Additional files
Supplementary files • Transparent reporting form

Data availability
The ribosome profiling data obtained in this study (GSE179854 and GSE200172) were deposited to the National Center for Biotechnology Information (NCBI). The proteome data for ProSeAM SILAC (ID: PXD026813) were available via ProteomeXchange. The structural coordinates (PDB: 7F5S) and cryo-EM maps (EMDB: EMD-31465) of His245 methylation-deficient ribosomes have been deposited in the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB), respectively.